Abstract Motivation Structure based ligand discovery is one of the most successful approaches for augmenting the drug discovery process. Currently, there is a notable shift towards machine learning (ML) methodologies to aid such procedures. Deep learning has recently gained considerable attention as it allows the model to “learn” to extract features that are relevant for the task at hand. Results We have developed a novel deep neural network estimating the binding affinity of ligand-receptor complexes. The complex is represented with a 3D grid, and the model utilizes a 3D convolution to produce a feature map of this representation, treating the atoms of both proteins and ligands in the same manner. Our network was tested on the CASF-2013 “scoring power” benchmark and Astex Diverse Set and outperformed classical scoring functions. Availability The model, together with usage instructions and examples, is available as a git repository at http://gitlab.com/cheminfIBB/pafnucy Contact firstname.lastname@example.org Supplementary information Supplementary data are available at Bioinformatics online. © The Author(s) 2018. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Bioinformatics – Oxford University Press
Published: May 10, 2018
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